1. There are times the site will remove bot replies. Therefore the reply count will be off.
The algorithm is pretty thorough on that in fact. I haven't seen a bot reply in a very long time. Bot posting is a different matter.
2. Also once a reply is removed, in any way, the reply count as well will not be rolled back.
So someone can comment then delete it. And the count can remain the same and there will be no sign of the comment.
3. I used to frequently use this fact, by removing all replies as well as the comment, so that it seems like no one has replied. The reply count will still be the same however.
Why remove the whole thread? Well they can no longer receive notifications. And the trolling usually stops because there's nothing visible to notify on.
On all of this there is a delay factor.
Should mention, that the reason for some of this, has a lot to do with reputation calculations, hidden behind the algorithm process. If the poster deletes a whole bunch, like I have, some of the calculations can't be undone. And negative reputation doesn't make any sense and division by zero is impossible.😆
